Starting phenix.real_space_refine on Wed Sep 17 15:43:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr3_61747/09_2025/9jr3_61747.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.572 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6056 2.51 5 N 1618 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9455 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2865 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 345} Chain breaks: 5 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1722 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1727 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.23 Number of scatterers: 9455 At special positions: 0 Unit cell: (84.624, 123, 161.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1721 8.00 N 1618 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 176 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 287.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 39.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.553A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 removed outlier: 3.539A pdb=" N HIS R 216 " --> pdb=" O ARG R 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 213 through 216' Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.859A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 347 removed outlier: 3.924A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.711A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 removed outlier: 4.021A pdb=" N LYS R 405 " --> pdb=" O GLN R 401 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 450 removed outlier: 3.547A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 459 Processing helix chain 'R' and resid 463 through 482 Processing helix chain 'P' and resid 2 through 17 removed outlier: 3.505A pdb=" N LYS P 13 " --> pdb=" O HIS P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 34 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.771A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.934A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.609A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.681A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.919A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.095A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.617A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 76 removed outlier: 7.122A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.200A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.843A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.655A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.036A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.496A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.592A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.713A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.714A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.921A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 146 493 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3031 1.34 - 1.46: 2489 1.46 - 1.58: 4065 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 9671 Sorted by residual: bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN G 11 " pdb=" CA GLN G 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N VAL S 2 " pdb=" CA VAL S 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N VAL A 5 " pdb=" CA VAL A 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N PHE P 34 " pdb=" CA PHE P 34 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 9666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 12626 1.09 - 2.18: 437 2.18 - 3.26: 48 3.26 - 4.35: 30 4.35 - 5.44: 2 Bond angle restraints: 13143 Sorted by residual: angle pdb=" C LYS A 95 " pdb=" N TRP A 96 " pdb=" CA TRP A 96 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" N PRO A 180 " pdb=" CA PRO A 180 " pdb=" C PRO A 180 " ideal model delta sigma weight residual 114.92 111.63 3.29 1.19e+00 7.06e-01 7.66e+00 angle pdb=" CA ILE R 310 " pdb=" C ILE R 310 " pdb=" N PHE R 311 " ideal model delta sigma weight residual 116.60 119.88 -3.28 1.45e+00 4.76e-01 5.12e+00 angle pdb=" CA SER S 181 " pdb=" C SER S 181 " pdb=" N ASN S 182 " ideal model delta sigma weight residual 116.84 120.59 -3.75 1.71e+00 3.42e-01 4.80e+00 angle pdb=" N TRP A 96 " pdb=" CA TRP A 96 " pdb=" C TRP A 96 " ideal model delta sigma weight residual 110.80 106.52 4.28 2.13e+00 2.20e-01 4.05e+00 ... (remaining 13138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 5048 16.06 - 32.12: 459 32.12 - 48.18: 121 48.18 - 64.25: 34 64.25 - 80.31: 6 Dihedral angle restraints: 5668 sinusoidal: 2103 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual -86.00 -158.47 72.47 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ASP A 199 " pdb=" C ASP A 199 " pdb=" N ILE A 200 " pdb=" CA ILE A 200 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.42 32.58 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1091 0.036 - 0.073: 298 0.073 - 0.109: 78 0.109 - 0.146: 25 0.146 - 0.182: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.71e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 176 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1490 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO S 107 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO G 49 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO S 173 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " 0.022 5.00e-02 4.00e+02 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 194 2.69 - 3.24: 9256 3.24 - 3.79: 14973 3.79 - 4.35: 20611 4.35 - 4.90: 33906 Nonbonded interactions: 78940 Sorted by model distance: nonbonded pdb=" O GLU R 302 " pdb=" O HOH R 601 " model vdw 2.136 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.192 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O GLY B 288 " model vdw 2.260 3.040 nonbonded pdb=" O SER R 341 " pdb=" OG1 THR R 345 " model vdw 2.303 3.040 ... (remaining 78935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.630 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 9680 Z= 0.169 Angle : 0.491 5.440 13161 Z= 0.277 Chirality : 0.039 0.182 1493 Planarity : 0.004 0.052 1656 Dihedral : 13.980 80.306 3348 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 0.62 % Allowed : 11.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1200 helix: 1.51 (0.26), residues: 436 sheet: -0.33 (0.32), residues: 259 loop : -0.49 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.009 0.001 TYR R 191 PHE 0.009 0.001 PHE R 335 TRP 0.011 0.001 TRP R 298 HIS 0.005 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9671) covalent geometry : angle 0.49068 (13143) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.46721 ( 12) hydrogen bonds : bond 0.17874 ( 493) hydrogen bonds : angle 6.60418 ( 1374) Misc. bond : bond 0.10668 ( 1) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 1.27680 ( 3) link_NAG-ASN : bond 0.00341 ( 1) link_NAG-ASN : angle 0.73955 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.387 Fit side-chains REVERT: R 32 MET cc_start: 0.5891 (mtp) cc_final: 0.5020 (ttm) REVERT: R 189 MET cc_start: 0.6155 (mmm) cc_final: 0.5929 (mmm) REVERT: R 201 SER cc_start: 0.6297 (m) cc_final: 0.6072 (p) REVERT: R 213 ARG cc_start: 0.6087 (mtt180) cc_final: 0.5485 (mtp180) REVERT: R 214 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5691 (mmm-85) REVERT: R 231 MET cc_start: 0.7273 (mtp) cc_final: 0.7020 (mtm) REVERT: R 312 MET cc_start: 0.5307 (mmm) cc_final: 0.4925 (mtp) REVERT: R 431 GLU cc_start: 0.6475 (tt0) cc_final: 0.6017 (tt0) REVERT: R 438 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6655 (mm-40) REVERT: R 455 VAL cc_start: 0.7784 (t) cc_final: 0.7520 (m) REVERT: P 8 MET cc_start: 0.6380 (ttp) cc_final: 0.6174 (ttp) REVERT: A 14 GLU cc_start: 0.5639 (tt0) cc_final: 0.5289 (mt-10) REVERT: A 17 LYS cc_start: 0.4326 (mttm) cc_final: 0.3643 (mtpt) REVERT: A 21 LYS cc_start: 0.4484 (tttm) cc_final: 0.3749 (mmpt) REVERT: A 73 LYS cc_start: 0.5898 (mttp) cc_final: 0.5234 (pmtt) REVERT: A 103 VAL cc_start: 0.7336 (t) cc_final: 0.7078 (p) REVERT: A 126 LYS cc_start: 0.4865 (ttmt) cc_final: 0.4039 (pptt) REVERT: A 188 ARG cc_start: 0.3888 (ttp80) cc_final: 0.3628 (ptm160) REVERT: A 196 GLU cc_start: 0.3461 (mm-30) cc_final: 0.2714 (mm-30) REVERT: A 238 MET cc_start: 0.6154 (mtm) cc_final: 0.5593 (ptm) REVERT: A 241 ARG cc_start: 0.6556 (ttm-80) cc_final: 0.6339 (mtm-85) REVERT: B 78 LYS cc_start: 0.6642 (ttmm) cc_final: 0.6353 (tppt) REVERT: B 98 SER cc_start: 0.7454 (p) cc_final: 0.7233 (p) REVERT: B 137 ARG cc_start: 0.4929 (tpp-160) cc_final: 0.4350 (tpt90) REVERT: B 146 LEU cc_start: 0.7948 (mt) cc_final: 0.7393 (tp) REVERT: B 177 THR cc_start: 0.7772 (m) cc_final: 0.7414 (p) REVERT: B 219 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6557 (mmt-90) REVERT: B 277 SER cc_start: 0.7749 (t) cc_final: 0.7102 (m) REVERT: B 285 LEU cc_start: 0.6636 (tp) cc_final: 0.6323 (tm) REVERT: B 325 MET cc_start: 0.6274 (tpp) cc_final: 0.5947 (tpp) REVERT: S 18 ARG cc_start: 0.4421 (ttm-80) cc_final: 0.4199 (ttt90) REVERT: S 222 GLU cc_start: 0.6506 (pt0) cc_final: 0.5712 (mm-30) outliers start: 6 outliers final: 1 residues processed: 197 average time/residue: 0.6108 time to fit residues: 128.8449 Evaluate side-chains 151 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 GLN R 216 HIS R 225 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 442 HIS P 6 GLN A 43 ASN A 229 ASN B 32 GLN B 35 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 239 ASN B 268 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.210772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171757 restraints weight = 10387.727| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.65 r_work: 0.3775 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 9680 Z= 0.293 Angle : 0.723 8.538 13161 Z= 0.383 Chirality : 0.049 0.202 1493 Planarity : 0.006 0.059 1656 Dihedral : 5.098 31.038 1367 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 4.16 % Allowed : 15.38 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.24), residues: 1200 helix: 1.14 (0.23), residues: 442 sheet: -0.23 (0.31), residues: 271 loop : -0.57 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 132 TYR 0.019 0.002 TYR R 297 PHE 0.027 0.003 PHE A 215 TRP 0.016 0.002 TRP B 169 HIS 0.009 0.002 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 9671) covalent geometry : angle 0.72234 (13143) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.14692 ( 12) hydrogen bonds : bond 0.06098 ( 493) hydrogen bonds : angle 5.23223 ( 1374) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.01107 ( 1) link_BETA1-4 : angle 0.96016 ( 3) link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 1.76268 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: R 32 MET cc_start: 0.6209 (mtp) cc_final: 0.5890 (ttm) REVERT: A 17 LYS cc_start: 0.6888 (mttm) cc_final: 0.6127 (mtpt) REVERT: A 21 LYS cc_start: 0.6434 (tttm) cc_final: 0.5741 (mmpt) REVERT: A 22 ASN cc_start: 0.7016 (m-40) cc_final: 0.6815 (m110) REVERT: A 43 ASN cc_start: 0.5445 (OUTLIER) cc_final: 0.4711 (m-40) REVERT: A 73 LYS cc_start: 0.6011 (mttp) cc_final: 0.5596 (pmtt) REVERT: A 196 GLU cc_start: 0.5230 (mm-30) cc_final: 0.4208 (mm-30) REVERT: A 246 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.6953 (t) REVERT: B 78 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8287 (tppt) REVERT: B 146 LEU cc_start: 0.8291 (mt) cc_final: 0.8026 (tp) REVERT: S 198 THR cc_start: 0.4493 (OUTLIER) cc_final: 0.4101 (p) outliers start: 40 outliers final: 17 residues processed: 174 average time/residue: 0.5798 time to fit residues: 108.4783 Evaluate side-chains 159 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 334 VAL Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.212279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173047 restraints weight = 10389.111| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.63 r_work: 0.3826 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9680 Z= 0.158 Angle : 0.572 7.997 13161 Z= 0.306 Chirality : 0.043 0.173 1493 Planarity : 0.004 0.055 1656 Dihedral : 4.791 34.163 1367 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 4.37 % Allowed : 17.78 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1200 helix: 1.55 (0.24), residues: 445 sheet: -0.14 (0.32), residues: 260 loop : -0.59 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.013 0.001 TYR R 191 PHE 0.015 0.002 PHE R 335 TRP 0.015 0.002 TRP A 96 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9671) covalent geometry : angle 0.57068 (13143) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.75326 ( 12) hydrogen bonds : bond 0.04842 ( 493) hydrogen bonds : angle 4.80719 ( 1374) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00783 ( 1) link_BETA1-4 : angle 0.65521 ( 3) link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 2.15164 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.385 Fit side-chains REVERT: R 32 MET cc_start: 0.6256 (mtp) cc_final: 0.5940 (ttm) REVERT: R 115 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 17 LYS cc_start: 0.6669 (mttm) cc_final: 0.5947 (mtpt) REVERT: A 21 LYS cc_start: 0.6346 (tttm) cc_final: 0.5674 (mmpt) REVERT: A 43 ASN cc_start: 0.5495 (OUTLIER) cc_final: 0.4512 (t0) REVERT: A 73 LYS cc_start: 0.5851 (mttp) cc_final: 0.5497 (pttt) REVERT: A 126 LYS cc_start: 0.6259 (ttmt) cc_final: 0.5250 (pptt) REVERT: A 188 ARG cc_start: 0.5237 (ptm160) cc_final: 0.5014 (ptm160) REVERT: A 196 GLU cc_start: 0.4943 (mm-30) cc_final: 0.3935 (mm-30) REVERT: B 78 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (tppt) REVERT: B 146 LEU cc_start: 0.8189 (mt) cc_final: 0.7987 (tp) REVERT: S 198 THR cc_start: 0.4340 (OUTLIER) cc_final: 0.3931 (p) REVERT: S 222 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6865 (mt-10) outliers start: 42 outliers final: 21 residues processed: 161 average time/residue: 0.6268 time to fit residues: 107.8832 Evaluate side-chains 154 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 6 optimal weight: 40.0000 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.214429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175674 restraints weight = 10426.159| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.63 r_work: 0.3852 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9680 Z= 0.123 Angle : 0.529 8.149 13161 Z= 0.284 Chirality : 0.041 0.165 1493 Planarity : 0.004 0.050 1656 Dihedral : 4.439 28.450 1366 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 5.09 % Allowed : 16.94 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.24), residues: 1200 helix: 1.89 (0.24), residues: 447 sheet: -0.09 (0.32), residues: 260 loop : -0.53 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.033 0.001 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.014 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9671) covalent geometry : angle 0.52798 (13143) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.61869 ( 12) hydrogen bonds : bond 0.04274 ( 493) hydrogen bonds : angle 4.55609 ( 1374) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00825 ( 1) link_BETA1-4 : angle 0.72325 ( 3) link_NAG-ASN : bond 0.00207 ( 1) link_NAG-ASN : angle 2.09795 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.414 Fit side-chains REVERT: R 32 MET cc_start: 0.6188 (mtp) cc_final: 0.5869 (ttm) REVERT: R 115 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 17 LYS cc_start: 0.6638 (mttm) cc_final: 0.5931 (mtpt) REVERT: A 21 LYS cc_start: 0.6285 (tttm) cc_final: 0.5638 (mmpt) REVERT: A 43 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.4366 (t0) REVERT: A 126 LYS cc_start: 0.6308 (ttmt) cc_final: 0.5306 (pptt) REVERT: A 196 GLU cc_start: 0.4891 (mm-30) cc_final: 0.3929 (mm-30) REVERT: B 78 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8139 (tppt) REVERT: S 192 SER cc_start: 0.7387 (t) cc_final: 0.7127 (m) REVERT: S 198 THR cc_start: 0.4316 (OUTLIER) cc_final: 0.3920 (p) REVERT: S 222 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6866 (mt-10) outliers start: 49 outliers final: 25 residues processed: 166 average time/residue: 0.5982 time to fit residues: 106.5472 Evaluate side-chains 158 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 40.0000 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.210139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170738 restraints weight = 10381.616| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.65 r_work: 0.3794 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9680 Z= 0.203 Angle : 0.611 7.873 13161 Z= 0.321 Chirality : 0.044 0.163 1493 Planarity : 0.004 0.052 1656 Dihedral : 4.724 27.492 1366 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 4.68 % Allowed : 18.40 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1200 helix: 1.73 (0.24), residues: 446 sheet: -0.14 (0.32), residues: 260 loop : -0.56 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.018 0.002 TYR R 191 PHE 0.021 0.002 PHE R 453 TRP 0.012 0.002 TRP B 169 HIS 0.006 0.002 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9671) covalent geometry : angle 0.61010 (13143) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.64011 ( 12) hydrogen bonds : bond 0.04905 ( 493) hydrogen bonds : angle 4.77021 ( 1374) Misc. bond : bond 0.00022 ( 1) link_BETA1-4 : bond 0.00752 ( 1) link_BETA1-4 : angle 0.82438 ( 3) link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 1.92211 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.390 Fit side-chains REVERT: R 32 MET cc_start: 0.6139 (mtp) cc_final: 0.5796 (ttm) REVERT: R 115 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 180 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6387 (mt-10) REVERT: A 17 LYS cc_start: 0.6668 (mmtm) cc_final: 0.5932 (mtpt) REVERT: A 21 LYS cc_start: 0.6415 (tttm) cc_final: 0.5700 (mmpt) REVERT: A 43 ASN cc_start: 0.5912 (OUTLIER) cc_final: 0.4259 (t0) REVERT: A 126 LYS cc_start: 0.6316 (ttmt) cc_final: 0.5285 (pptt) REVERT: A 196 GLU cc_start: 0.5013 (mm-30) cc_final: 0.3965 (mm-30) REVERT: B 78 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8122 (tppt) REVERT: B 252 LEU cc_start: 0.7540 (tt) cc_final: 0.7262 (tp) REVERT: S 128 MET cc_start: 0.5766 (mpp) cc_final: 0.5509 (mpt) REVERT: S 192 SER cc_start: 0.7378 (t) cc_final: 0.7113 (m) REVERT: S 198 THR cc_start: 0.4426 (OUTLIER) cc_final: 0.4013 (p) REVERT: S 222 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6933 (mt-10) outliers start: 45 outliers final: 28 residues processed: 157 average time/residue: 0.6044 time to fit residues: 101.7710 Evaluate side-chains 167 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 47 optimal weight: 0.8980 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.213637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175107 restraints weight = 10325.615| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.69 r_work: 0.3820 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9680 Z= 0.126 Angle : 0.532 7.577 13161 Z= 0.283 Chirality : 0.041 0.162 1493 Planarity : 0.004 0.049 1656 Dihedral : 4.435 25.749 1366 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 4.05 % Allowed : 19.65 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1200 helix: 2.00 (0.24), residues: 447 sheet: -0.13 (0.32), residues: 260 loop : -0.53 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.018 0.001 TYR R 191 PHE 0.018 0.001 PHE R 335 TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9671) covalent geometry : angle 0.53125 (13143) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.56412 ( 12) hydrogen bonds : bond 0.04174 ( 493) hydrogen bonds : angle 4.49781 ( 1374) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00777 ( 1) link_BETA1-4 : angle 0.78253 ( 3) link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 2.05813 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.385 Fit side-chains REVERT: R 32 MET cc_start: 0.6103 (mtp) cc_final: 0.5823 (ttm) REVERT: R 115 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7391 (mp) REVERT: R 180 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6361 (mt-10) REVERT: A 17 LYS cc_start: 0.6564 (mmtm) cc_final: 0.5851 (mtpt) REVERT: A 126 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5222 (pptt) REVERT: A 196 GLU cc_start: 0.4795 (mm-30) cc_final: 0.3783 (mm-30) REVERT: B 252 LEU cc_start: 0.7422 (tt) cc_final: 0.7120 (tp) REVERT: S 192 SER cc_start: 0.7328 (t) cc_final: 0.7081 (m) REVERT: S 198 THR cc_start: 0.4269 (OUTLIER) cc_final: 0.3867 (p) REVERT: S 222 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6843 (mt-10) outliers start: 39 outliers final: 27 residues processed: 151 average time/residue: 0.5916 time to fit residues: 96.1126 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 8 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.214068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175725 restraints weight = 10347.717| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.69 r_work: 0.3844 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9680 Z= 0.114 Angle : 0.521 7.203 13161 Z= 0.276 Chirality : 0.041 0.164 1493 Planarity : 0.004 0.047 1656 Dihedral : 4.278 26.037 1366 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 3.53 % Allowed : 20.37 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1200 helix: 2.11 (0.24), residues: 447 sheet: -0.07 (0.33), residues: 245 loop : -0.47 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.027 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9671) covalent geometry : angle 0.51974 (13143) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.54220 ( 12) hydrogen bonds : bond 0.03958 ( 493) hydrogen bonds : angle 4.39415 ( 1374) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00728 ( 1) link_BETA1-4 : angle 0.79373 ( 3) link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 2.03677 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: R 32 MET cc_start: 0.6013 (mtp) cc_final: 0.5731 (ttm) REVERT: R 115 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 17 LYS cc_start: 0.6539 (mmtm) cc_final: 0.5826 (mtpt) REVERT: A 22 ASN cc_start: 0.6780 (m-40) cc_final: 0.6516 (m-40) REVERT: A 126 LYS cc_start: 0.6264 (ttmt) cc_final: 0.5245 (pptt) REVERT: A 196 GLU cc_start: 0.4755 (mm-30) cc_final: 0.3745 (mm-30) REVERT: B 252 LEU cc_start: 0.7356 (tt) cc_final: 0.7066 (tp) REVERT: S 128 MET cc_start: 0.5714 (mpp) cc_final: 0.5460 (mpt) REVERT: S 180 MET cc_start: 0.6016 (tpt) cc_final: 0.5658 (tpt) REVERT: S 192 SER cc_start: 0.7293 (t) cc_final: 0.7043 (m) REVERT: S 198 THR cc_start: 0.4225 (OUTLIER) cc_final: 0.3827 (p) outliers start: 34 outliers final: 25 residues processed: 151 average time/residue: 0.6145 time to fit residues: 99.8471 Evaluate side-chains 156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.214960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176794 restraints weight = 10403.978| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.65 r_work: 0.3841 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9680 Z= 0.119 Angle : 0.519 7.403 13161 Z= 0.276 Chirality : 0.041 0.156 1493 Planarity : 0.004 0.047 1656 Dihedral : 4.211 26.081 1366 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 4.05 % Allowed : 19.96 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.25), residues: 1200 helix: 2.18 (0.24), residues: 447 sheet: 0.08 (0.32), residues: 256 loop : -0.49 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 208 TYR 0.014 0.001 TYR R 191 PHE 0.026 0.001 PHE A 108 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9671) covalent geometry : angle 0.51811 (13143) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.54423 ( 12) hydrogen bonds : bond 0.03900 ( 493) hydrogen bonds : angle 4.32859 ( 1374) Misc. bond : bond 0.00010 ( 1) link_BETA1-4 : bond 0.00619 ( 1) link_BETA1-4 : angle 0.84680 ( 3) link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.97012 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 17 LYS cc_start: 0.6549 (mmtm) cc_final: 0.5839 (mtpt) REVERT: A 22 ASN cc_start: 0.6799 (m-40) cc_final: 0.6541 (m-40) REVERT: A 126 LYS cc_start: 0.6250 (ttmt) cc_final: 0.5258 (pptt) REVERT: A 196 GLU cc_start: 0.4814 (mm-30) cc_final: 0.3802 (mm-30) REVERT: B 252 LEU cc_start: 0.7385 (tt) cc_final: 0.7090 (tp) REVERT: S 83 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: S 180 MET cc_start: 0.6012 (tpt) cc_final: 0.5686 (tpt) REVERT: S 192 SER cc_start: 0.7285 (t) cc_final: 0.7027 (m) REVERT: S 198 THR cc_start: 0.4206 (OUTLIER) cc_final: 0.3820 (p) outliers start: 39 outliers final: 27 residues processed: 157 average time/residue: 0.6119 time to fit residues: 103.1329 Evaluate side-chains 156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 60 optimal weight: 9.9990 chunk 29 optimal weight: 0.0030 chunk 92 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.215404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176653 restraints weight = 10363.520| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.55 r_work: 0.3857 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9680 Z= 0.118 Angle : 0.534 9.624 13161 Z= 0.283 Chirality : 0.041 0.156 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.192 26.079 1366 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 4.37 % Allowed : 20.79 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1200 helix: 2.15 (0.24), residues: 447 sheet: 0.07 (0.33), residues: 247 loop : -0.41 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 208 TYR 0.018 0.001 TYR R 191 PHE 0.022 0.001 PHE R 453 TRP 0.026 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9671) covalent geometry : angle 0.53282 (13143) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.51881 ( 12) hydrogen bonds : bond 0.03881 ( 493) hydrogen bonds : angle 4.29851 ( 1374) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00801 ( 1) link_BETA1-4 : angle 0.86974 ( 3) link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.96319 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 17 LYS cc_start: 0.6489 (mmtm) cc_final: 0.5770 (mtpt) REVERT: A 126 LYS cc_start: 0.6239 (ttmt) cc_final: 0.5221 (pptt) REVERT: A 196 GLU cc_start: 0.4728 (mm-30) cc_final: 0.3718 (mm-30) REVERT: B 252 LEU cc_start: 0.7365 (tt) cc_final: 0.7085 (tp) REVERT: S 180 MET cc_start: 0.5974 (tpt) cc_final: 0.5635 (tpt) REVERT: S 192 SER cc_start: 0.7243 (t) cc_final: 0.7024 (m) REVERT: S 198 THR cc_start: 0.4191 (OUTLIER) cc_final: 0.3796 (p) outliers start: 42 outliers final: 31 residues processed: 154 average time/residue: 0.5581 time to fit residues: 92.9118 Evaluate side-chains 165 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.216153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177850 restraints weight = 10337.765| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.65 r_work: 0.3862 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9680 Z= 0.112 Angle : 0.524 7.020 13161 Z= 0.278 Chirality : 0.041 0.157 1493 Planarity : 0.004 0.045 1656 Dihedral : 4.114 26.200 1366 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1200 helix: 2.23 (0.24), residues: 447 sheet: 0.30 (0.33), residues: 249 loop : -0.48 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 208 TYR 0.014 0.001 TYR R 191 PHE 0.028 0.001 PHE A 108 TRP 0.031 0.001 TRP B 82 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9671) covalent geometry : angle 0.52343 (13143) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.53122 ( 12) hydrogen bonds : bond 0.03758 ( 493) hydrogen bonds : angle 4.23043 ( 1374) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00652 ( 1) link_BETA1-4 : angle 0.91328 ( 3) link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 1.86609 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: R 115 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7482 (mp) REVERT: R 177 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: R 213 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7247 (tpt90) REVERT: A 17 LYS cc_start: 0.6519 (mmtm) cc_final: 0.5807 (mtpt) REVERT: A 126 LYS cc_start: 0.6312 (ttmt) cc_final: 0.5338 (pptt) REVERT: A 196 GLU cc_start: 0.4715 (mm-30) cc_final: 0.3714 (mm-30) REVERT: B 252 LEU cc_start: 0.7341 (tt) cc_final: 0.7066 (tp) REVERT: S 83 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7054 (mtp) REVERT: S 180 MET cc_start: 0.5998 (tpt) cc_final: 0.5688 (tpt) REVERT: S 192 SER cc_start: 0.7257 (t) cc_final: 0.7055 (m) REVERT: S 198 THR cc_start: 0.4235 (OUTLIER) cc_final: 0.3818 (p) outliers start: 36 outliers final: 28 residues processed: 149 average time/residue: 0.5511 time to fit residues: 88.7316 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 3 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN P 6 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.215152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176272 restraints weight = 10279.748| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.56 r_work: 0.3859 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9680 Z= 0.129 Angle : 0.552 10.223 13161 Z= 0.290 Chirality : 0.042 0.164 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.171 26.244 1366 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 3.95 % Allowed : 21.31 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1200 helix: 2.17 (0.24), residues: 447 sheet: 0.11 (0.33), residues: 246 loop : -0.42 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 208 TYR 0.026 0.001 TYR R 191 PHE 0.026 0.001 PHE B 241 TRP 0.038 0.001 TRP B 82 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9671) covalent geometry : angle 0.55005 (13143) SS BOND : bond 0.00149 ( 6) SS BOND : angle 1.25836 ( 12) hydrogen bonds : bond 0.03886 ( 493) hydrogen bonds : angle 4.27380 ( 1374) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00620 ( 1) link_BETA1-4 : angle 0.92247 ( 3) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.82570 ( 3) =============================================================================== Job complete usr+sys time: 4550.11 seconds wall clock time: 78 minutes 26.48 seconds (4706.48 seconds total)